R/apply.antsImage.R

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

#' @rdname apply
#' @title Extension of apply to allow input of antsImage
#'
#' @description Returns an antsImage after applying function.
#'
#' @param X an antsImage
#' @param MARGIN a vector giving the subscripts which the function will be applied over.
#' @param FUN the function to be applied.
#' @param ...  optional arguments to FUN
#' @return output is antsImage of lower dimnesion than input
#' @author Duda JT
#' @examples
#'
#' img <- makeImage(c(4, 4, 4), rnorm(4 * 4 * 4))
#' img2 <- apply(img, c(1, 2), mean)
#' is.antsImage(img2)
#'
#' @export
apply <- function(X, MARGIN, FUN, ...) {
  UseMethod("apply")
}

#' @rdname apply
#' @export
apply.default <- function(X, MARGIN, FUN, ...) {
  base::apply(X = X, MARGIN = MARGIN, FUN = FUN, ...)
}

#' @rdname apply
#' @method apply antsImage
#' @export
apply.antsImage <- function(X, MARGIN, FUN, ...) {
  ar <- as.array(X)
  ar <- base::apply(X = ar, MARGIN = MARGIN, FUN = FUN, ...)

  if (length(MARGIN) > 1) {
    ar <- as.antsImage(ar)
    antsSetSpacing(ar, antsGetSpacing(X)[MARGIN])
    antsSetOrigin(ar, antsGetOrigin(X)[MARGIN])
    dir <- antsGetDirection(X)[MARGIN, MARGIN]
    #   BA: the code below is inconsistent with other ants approaches
    #   it also has the rather nasty effect of flipping images anatomically
    #   in some cases.
    #    for ( i in c(1:length(MARGIN)) )
    #      {
    #      if ( sum(dir[i,]) == 0 )
    #        {
    #        dir[i,i] = 1
    #        }
    #      }
    antsSetDirection(ar, dir)
  }

  return(ar)
}